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Human Virome

Year 2017, - Mikrobiyota, 44 - 49, 15.11.2017

Abstract

A healthy human body always contains a large number of foreign cells and viruses. The viral component of the human microbiome is called virome. It is the collection of all viruses in humans, viruses that cause acute, permanent or latent infection and including viruses such as endogenous retroviruses integrated into the human genome. It is assumed that viruses are often clinically silent and that they have found an ideal balance to prevent viral persistence and transfer, which would prevent them from responding to them. Some of the new viruses found to be advantageous to the main hosts. Most viruses are not constantly pathogenic and are always harmless, but they can cause different results depending on the health and immunological status of the host. Our knowledge about human virome expands as the studies in this subject increases. Using a new generation of diagnostic methods, analyzing virome within a few hours or even a few minutes from patient samples will provide faster diagnosis, treatment and control of diseases. Viruses and human virome have a very complex structure and need a wide range of studies. In this review; human virome types, where they can be found in the body, and the effects on human health will be discussed.

References

  • 1. Virgin HW, Wherry EJ, Ahmed R. Redefining chronic viral infection. Cell 2009;138:30–50.
  • 2. Relman DA. The human body as microbial observatory. Nat Genet 2002;30:131–133.
  • 3. Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 2007;449:811–818.
  • 4. Wylie, K.M., Weinstock, G.M., and Storch, G.A. Emerging view of the human virome. Transl. Res. 2012;160, 283–290.
  • 5. Chen EC, Miller SA, DeRisi JL, Chiu CY: Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J Vis Exp 2011. 50.
  • 6. Zou S, Caler L, Colombini-Hatch S, Glynn S, Srinivas P. Research on the human virome: where are we and what is next. Microbiome 2016;4:32.
  • 7. Nelson, K.E., J.L. Peterson, and S. Garges. Metagenomics of the human body, 2011; 63-77.
  • 8. Willner D, Furlan M, Haynes M, Schmieder R, Angly F, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 2009; 4(10):e7370.
  • 9. Zhang T, Breitbart M, Lee WH, Run J-Q, Wei CL, Soh SWL, Hibberd ML, Liu ET, Rohwer F, Ruan Y. RNA viral community in human feces: prevalence of plant pathogenic virüses. PLoS Biol 2005;4(1):e3.
  • 10. Lecuit, M., and Eloit, M. The human virome: new tools and concepts. Trends Microbiol. 2014; 21:510–515.
  • 11. Little JW Lysogeny, prophage induction, and lysogenic conversion. In: Waldor MK, Friedman DI, Adhya SL (eds) Phages: their role in bacterial pathogenesis and biotechnology. ASM Press, Washington, DC, 2005;37–54.
  • 12. Breitbart M, Rohwer F, Abedon ST Phage ecology and bacterial pathogenesis. In: Waldor MK, Friedman DI, Adhya SL (eds) Phages: their role in bacterial pathogenesis and biotechnolgy. ASM Press, Washington, DC, 2005;66–92.
  • 13. Stapleton JT, Williams CF, Xiang J. GB virüs type C: a beneficial infection? JClinMicrobiol 2004;42(9):3915–3919.
  • 14. Okamoto H. History of discoveries and pathogenicity of TT virüses. Curr Top Microbiol Immunol 2009;331:1–201–220.
  • 15. Foulongne, V., Sauvage, V., Hebert, C., Dereure, O., Cheval, J., Ar Gouilh, M., Pariente, K., Segondy, M., Burguière, A., Manuguerra, J.-C., Caro, V., Eloit, M. Human skin microbiota: High diversity of DNA virüses identifi ed in the human skin by high throughput sequencing. PLoS One 7, 2012; e38499.
  • 16. Dalianis T, Hirsch HH. Human polyomavi-ruses in disease and cancer. Virology 2013;437:63–72
  • 17. Feltkamp MC, Kazem S, van der Meijden E, Lauber C, Gorbalenya AE. From Stockholm to Malawi: recent developments in studying human polyomavirüses. J. Gen. Virol. 2013; 94:482–496.
  • 18. Smith DB, Purdy MA, Simmonds P. Genetic variability and theclassifi cation of hepatitis E virüs. J. Virol. 2013;87:4161–4169.
  • 19. Lhomme S, Abravanel F, Dubois M, Sandres Saune K, Rostaing L, Kamar N, Izopet J. HEV quasispecies and the outcome of acute hepatitis E in solid-organ transplant patients. J. Virol. 2012; 86:10006–10014.
  • 20. Kamar N, Bendall R, Legrand-Abravanel F, Xia NS, Ijaz S, Izopet J, Dalton HR. Hepatitis E. Lancet 2012; 379:2477–2488.
  • 21. Hino, S., and Miyata, H. Torque teno virüs (TTV): current status. Rev. Med. Virol. 2007;17, 45–57.
  • 22. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. Sequence analysis of the human virome in febrile and afebrile children. PLoS ONE. 2012; 7:e27735.
  • 23. Cadwell, K., Patel, K.K., Maloney, N.S., Liu, T.C., Ng, A.C., Storer, C.E., Head, R.D., Xavier, R., Stappenbeck, T.S., and Virgin, H.W. Virüs-plussusceptibility gene interaction determines Crohn’s disease gene Atg16L1 phenotypes in intestine. Cell 2010;141:1135–1145.
  • 24. D. Willner, M. Furlan, M. Haynes, R. Schmieder, F.E. Angly, J. Silva, et al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fi brosis and non-cystic fi brosis individuals PLoS One, 2009;4 e7370.
  • 25. Delwart E. Viruses of the Human Body: Some of our resident viruses may be benefi cial. The Scientist. 2016;30(11): e 47291
  • 26. Lazarczyk, M., Cassonnet, P., Pons, C., Jacob, Y., Favre, M. The EVER proteins as a natural barrier against papillomavirüses: a new insight into the pathogenesis of human papillomavirüs infections. Microbiol. Mol. Biol. Rev. 2009;73, 348–370.
  • 27. Bhattarai, N., and J. T. Stapleton. GB virüs C: the good boy virüs? Trends Microbiol. 2012;20: 124–130.
  • 28. Delwart EL Viral metagenomics. Rev Med Virol 2007;17: 115–131
  • 29. Woolhouse ME, Howey R, Gaunt E, Reilly L, Chase-Topping M, Savill N. Temporal trends in the discovery of human virüses. Proc Biol Sci. 2008; 275:2111–2115.
  • 30. Wang D, Coscoy L, Zylberberg M, et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002; 99:15687–15692.
  • 31. Wang D, Urisman A, Liu YT, et al. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003; 1:E2.

İnsan Viromu

Year 2017, - Mikrobiyota, 44 - 49, 15.11.2017

Abstract

Sağlıklı insan vücudu her zaman çok sayıda yabancı hücre ve virüs içermektedir. İnsan mikrobiyomunun viral bileşeni virom olarak adlandırılır. Akut, kalıcı veya latent enfeksiyona neden olan virüsler ve insan genomuna entegre edilmiş endojen retrovirüsler gibi virüsler de dahil olmak üzere insanlarda bulunan tüm virüslerin toplanmasıdır. Virüslerin sıklıkla klinik olarak sessiz oldukları ve konağın kendilerine karşı koymasını önleyecek, viral kalıcılığa ve aktarıma katkıda bulunacak ideal bir denge buldukları varsayılmıştır. Bulunan yeni virüslerin bazısında ise ana konakçılarına avantaj sağladıkları ortaya çıkmıştır. Çoğu virüs sürekli patojen değildir ve daima zararsızdır fakat konağın sağlık ve immünolojik durumlarına bağlı olarak farklı sonuçlara neden olabilir. İnsan viromu hakkındaki bilgilerimiz bu konudaki çalışmalar arttıkça genişlemektedir. Yeni nesil tanı yöntemleri kullanarak hasta örneklerinden viromunu birkaç saat hatta birkaç dakika içinde analiz etme hastalıkların daha hızlı tanı, tedavi ve kontrolünü sağlayacaktır. Virüsler ve insan viromu çok karmaşık yapıya sahip olup bu konuda yapılacak geniş çaplı çalışmalara ihtiyaç duyulmaktadır. Bu derlemede; insan viromu tipleri, vücutta bulunabileceği yerler ve insan sağlığına etkileri tartışılacaktır.

References

  • 1. Virgin HW, Wherry EJ, Ahmed R. Redefining chronic viral infection. Cell 2009;138:30–50.
  • 2. Relman DA. The human body as microbial observatory. Nat Genet 2002;30:131–133.
  • 3. Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 2007;449:811–818.
  • 4. Wylie, K.M., Weinstock, G.M., and Storch, G.A. Emerging view of the human virome. Transl. Res. 2012;160, 283–290.
  • 5. Chen EC, Miller SA, DeRisi JL, Chiu CY: Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J Vis Exp 2011. 50.
  • 6. Zou S, Caler L, Colombini-Hatch S, Glynn S, Srinivas P. Research on the human virome: where are we and what is next. Microbiome 2016;4:32.
  • 7. Nelson, K.E., J.L. Peterson, and S. Garges. Metagenomics of the human body, 2011; 63-77.
  • 8. Willner D, Furlan M, Haynes M, Schmieder R, Angly F, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 2009; 4(10):e7370.
  • 9. Zhang T, Breitbart M, Lee WH, Run J-Q, Wei CL, Soh SWL, Hibberd ML, Liu ET, Rohwer F, Ruan Y. RNA viral community in human feces: prevalence of plant pathogenic virüses. PLoS Biol 2005;4(1):e3.
  • 10. Lecuit, M., and Eloit, M. The human virome: new tools and concepts. Trends Microbiol. 2014; 21:510–515.
  • 11. Little JW Lysogeny, prophage induction, and lysogenic conversion. In: Waldor MK, Friedman DI, Adhya SL (eds) Phages: their role in bacterial pathogenesis and biotechnology. ASM Press, Washington, DC, 2005;37–54.
  • 12. Breitbart M, Rohwer F, Abedon ST Phage ecology and bacterial pathogenesis. In: Waldor MK, Friedman DI, Adhya SL (eds) Phages: their role in bacterial pathogenesis and biotechnolgy. ASM Press, Washington, DC, 2005;66–92.
  • 13. Stapleton JT, Williams CF, Xiang J. GB virüs type C: a beneficial infection? JClinMicrobiol 2004;42(9):3915–3919.
  • 14. Okamoto H. History of discoveries and pathogenicity of TT virüses. Curr Top Microbiol Immunol 2009;331:1–201–220.
  • 15. Foulongne, V., Sauvage, V., Hebert, C., Dereure, O., Cheval, J., Ar Gouilh, M., Pariente, K., Segondy, M., Burguière, A., Manuguerra, J.-C., Caro, V., Eloit, M. Human skin microbiota: High diversity of DNA virüses identifi ed in the human skin by high throughput sequencing. PLoS One 7, 2012; e38499.
  • 16. Dalianis T, Hirsch HH. Human polyomavi-ruses in disease and cancer. Virology 2013;437:63–72
  • 17. Feltkamp MC, Kazem S, van der Meijden E, Lauber C, Gorbalenya AE. From Stockholm to Malawi: recent developments in studying human polyomavirüses. J. Gen. Virol. 2013; 94:482–496.
  • 18. Smith DB, Purdy MA, Simmonds P. Genetic variability and theclassifi cation of hepatitis E virüs. J. Virol. 2013;87:4161–4169.
  • 19. Lhomme S, Abravanel F, Dubois M, Sandres Saune K, Rostaing L, Kamar N, Izopet J. HEV quasispecies and the outcome of acute hepatitis E in solid-organ transplant patients. J. Virol. 2012; 86:10006–10014.
  • 20. Kamar N, Bendall R, Legrand-Abravanel F, Xia NS, Ijaz S, Izopet J, Dalton HR. Hepatitis E. Lancet 2012; 379:2477–2488.
  • 21. Hino, S., and Miyata, H. Torque teno virüs (TTV): current status. Rev. Med. Virol. 2007;17, 45–57.
  • 22. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. Sequence analysis of the human virome in febrile and afebrile children. PLoS ONE. 2012; 7:e27735.
  • 23. Cadwell, K., Patel, K.K., Maloney, N.S., Liu, T.C., Ng, A.C., Storer, C.E., Head, R.D., Xavier, R., Stappenbeck, T.S., and Virgin, H.W. Virüs-plussusceptibility gene interaction determines Crohn’s disease gene Atg16L1 phenotypes in intestine. Cell 2010;141:1135–1145.
  • 24. D. Willner, M. Furlan, M. Haynes, R. Schmieder, F.E. Angly, J. Silva, et al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fi brosis and non-cystic fi brosis individuals PLoS One, 2009;4 e7370.
  • 25. Delwart E. Viruses of the Human Body: Some of our resident viruses may be benefi cial. The Scientist. 2016;30(11): e 47291
  • 26. Lazarczyk, M., Cassonnet, P., Pons, C., Jacob, Y., Favre, M. The EVER proteins as a natural barrier against papillomavirüses: a new insight into the pathogenesis of human papillomavirüs infections. Microbiol. Mol. Biol. Rev. 2009;73, 348–370.
  • 27. Bhattarai, N., and J. T. Stapleton. GB virüs C: the good boy virüs? Trends Microbiol. 2012;20: 124–130.
  • 28. Delwart EL Viral metagenomics. Rev Med Virol 2007;17: 115–131
  • 29. Woolhouse ME, Howey R, Gaunt E, Reilly L, Chase-Topping M, Savill N. Temporal trends in the discovery of human virüses. Proc Biol Sci. 2008; 275:2111–2115.
  • 30. Wang D, Coscoy L, Zylberberg M, et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002; 99:15687–15692.
  • 31. Wang D, Urisman A, Liu YT, et al. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003; 1:E2.
There are 31 citations in total.

Details

Primary Language Turkish
Subjects Health Care Administration
Journal Section Review
Authors

Semra Öz

Mustafa Altındiş

Publication Date November 15, 2017
Acceptance Date October 26, 2017
Published in Issue Year 2017 - Mikrobiyota

Cite

AMA Öz S, Altındiş M. İnsan Viromu. J Biotechnol and Strategic Health Res. November 2017;1:44-49.

Journal of Biotechnology and Strategic Health Research